Add methyl probe annotations liftover process description

analyses/methylation-summary/01-calculate-tpm-medians.R

@@ -21,7 +21,7 @@ option_list <- list(
               help = "OpenPedCan rnaseq tpm gene or isoform matrix file",
               metavar = "character"),
   make_option(opt_str = "--methyl_probe_annot", type = "character", default = NULL,
-              help = "Methyl gencode array probe annotation results file",
+              help = "Methyl gencode array probe annotations",
               metavar = "character"),
   make_option(opt_str = "--methyl_independent_samples", type = "character", default = NULL,
               help = "OpenPedCan methyl independent biospecimen list file",

analyses/methylation-summary/02-calculate-methly-quantiles.R

@@ -20,7 +20,7 @@ option_list <- list(
               help = "OPenPedCan methyl beta-values or m-values matrix file",
               metavar = "character"),
   make_option(opt_str = "--methyl_probe_annot", type = "character", default = NULL,
-              help = "Methyl gencode array probe annotation results file",
+              help = "Methyl gencode array probe annotations",
               metavar = "character"),
   make_option(opt_str = "--independent_samples", type = "character", default = NULL,
               help = "OpenPedCan methyl independent biospecimen list file",

analyses/methylation-summary/03-methyl-tpm-correlation.py

@@ -35,7 +35,7 @@ def read_parameters():
 	p.add_argument('METHYL_INDEPENDENT_SAMPLES', type=str, default=None, help="OPenPedCan methyl independent biospecimen list file\n\n")
 	p.add_argument('METHLY_MATRIX', type=str, default=None, help="OpenPedCan methyl beta-values or m-values matrix file\n\n")
 	p.add_argument('EXP_MATRIX', type=str, default=None, help="OPenPedCan expression matrix file\n\n")
-	p.add_argument('PROBE_ANNOT', type=str, default=None, help="Methylation aaray probe gencode annotation results file\n\n")
+	p.add_argument('PROBE_ANNOT', type=str, default=None, help="Methyl gencode array probe annotations\n\n")
 	p.add_argument('-m', '--methyl_values', type=str, default='beta', choices=METHLY_VALUES, help="OpenPedCan methly matrix values: beta (default) and m\n\n")
 	p.add_argument('-e', '--exp_values', type=str, default='gene', choices=EXP_TYPE, help="OpenPedCan expression matrix values: gene (default) and isoform\n\n")
 	p.add_argument('-v', '--version', action='version', version="03-methyl-tpm-correlation.py version {} ({})".format(__version__, __date__), help="Print the current 03-methyl-tpm-correlation.py version and exit\n\n")

analyses/methylation-summary/04-tpm-transcript-representation.py

@@ -31,7 +31,7 @@ def read_parameters():
 	p.add_argument('METHYL_INDEPENDENT_SAMPLES', type=str, default=None, help="OPenPedCan methyl independent biospecimen list file\n\n")
 	p.add_argument('GENE_EXP_MATRIX', type=str, default=None, help="OPenPedCan gene expression matrix file\n\n")
 	p.add_argument('ISOFORM_EXP_MATRIX', type=str, default=None, help="OPenPedCan isoform expression matrix file\n\n")
-	p.add_argument('PROBE_ANNOT', type=str, default=None, help="Methylation array probe gencode annotation results file\n\n")
+	p.add_argument('PROBE_ANNOT', type=str, default=None, help="Methyl gencode array probe annotations\n\n")
 	p.add_argument('-v', '--version', action='version', version="04-tpm-transcript-representation.py version {} ({})".format(__version__, __date__), help="Print the current 04-tpm-transcript-representation.py version and exit\n\n")
 	return p.parse_args()
 

analyses/methylation-summary/05-create-methyl-summary-table.R

@@ -25,7 +25,7 @@ option_list <- list(
               help = "Methyl array probe beta/m-values quantiles results file",
               metavar = "character"),
   make_option(opt_str = "--methyl_probe_annot", type = "character", default = NULL,
-              help = "Methyl gencode array probe annotation results file",
+              help = "Methyl gencode array probe annotations",
               metavar = "character"),
   make_option(opt_str = "--rnaseq_tpm_medians", type = "character", default = NULL,
               help = "RNA-Seq gene-level or isoform-level tmp median expression results file",

analyses/methylation-summary/README.md

@@ -2,7 +2,10 @@
 
 ## Purpose
 
-Summarize preprocessed `Illumina Infinium HumanMethylation` array measurements produced by the [OpenPedCan methylation-preprocessing module](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/methylation-preprocessing) and [Illumina infinium methylation array CpG probe coordinates](https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html) lifted-over from GRCh37 to GRCh38 build and annotated with GENCODE v39 release that is currently utilized in the OpenPedCan data analyses.
+Summarize preprocessed `Illumina Infinium Human Methylation` array measurements produced by the [OpenPedCan methylation-preprocessing module](https://github.com/PediatricOpenTargets/OpenPedCan-analysis/tree/dev/analyses/methylation-preprocessing) and [Illumina infinium methylation array CpG probe coordinates](https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html) lifted-over from `GRCh37` to `GRCh38` build and annotated with [GENCODE v39 release](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/) that is currently utilized in the OpenPedCan data analyses.
+
+## Methylation array CpG probe coordinates liftover
+The 450K and EPIC Illumina Infinium methylation array CpG probe coordinates are based on the `Human Build 37 (GRCh37/hg19)` genome assembly. Probe coordinates were converted to `Human Build 38 (GRCh38/hg38)` using the [ENSEMBL Assembly Converter tool](https://useast.ensembl.org/Homo_sapiens/Tools/AssemblyConverter). A probe annotation file, `infinium.gencode.v39.probe.annotations.tsv` currently used in the module analyses, was created by annotating all the probes that were lifted over with associated gene features (i.e., `promoter`, `5' UTR`, `exon`, `intron`, `3'UTR`, and `intergenic`) based on `GENCODE v39` release. Intron coordinates, typically not included in the GFF3/GTF genome annotation formats, were added to the GENCODE annotations file using [GenomeTools](http://genometools.org/). Probe locations were then assigned with their intersecting gene annotation features with [bedtools](https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html). 
 
 
 ## Analysis scripts
@@ -19,7 +22,7 @@ Options:
     OpenPedCan rnaseq tpm gene or isoform matrix file
 
  --methyl_probe_annot=CHARACTER
-    Methyl gencode array probe annotation results file
+    Methyl gencode array probe annotations
 
   --methyl_independent_samples=CHARACTER
     OpenPedCan methyl independent biospecimen list file
@@ -46,7 +49,7 @@ Options:
 		OPenPedCan methyl beta-values or m-values matrix file
 
  --methyl_probe_annot=CHARACTER
-    Methyl gencode array probe annotation results file
+    Methyl gencode array probe annotations
 
 	--independent_samples=CHARACTER
 		OpenPedCan methyl independent biospecimen list file
@@ -78,7 +81,7 @@ positional arguments:
 
   EXP_MATRIX            OPenPedCan expression matrix file
 
-  PROBE_ANNOT           Methylation aaray probe gencode annotation results file
+  PROBE_ANNOT           Methyl gencode array probe annotations
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -129,7 +132,7 @@ positional arguments:
 
   ISOFORM_EXP_MATRIX    OPenPedCan isoform expression matrix file
 
-  PROBE_ANNOT           Methylation aaray probe gencode annotation results file
+  PROBE_ANNOT           Methyl gencode array probe annotations
 
   -v, --version         Print the current 04-tpm-transcript-representation.py version and exit
 ```
@@ -168,7 +171,7 @@ Options:
 		Methyl array probe beta/m-values quantiles results file
 
 	--methyl_probe_annot=CHARACTER
-		Methyl gencode array probe annotation results file
+		Methyl gencode array probe annotations
 
   --rnaseq_tpm_medians=CHARACTER
     RNA-Seq gene-level or isoform-level tmp median expression results file